Creating alternate Bed file by incorporating INDELs locations

Question

[ersgupta]

I have a exome bed file (coordinates wrt to ref genome) and a bed file with coordinates of INDELs (incorporated in ref genome). Now I want to generate a modified exome bed file which can shift the coordinates wrt to INDEL event.

For example

exome bed file:

chr1 10 100
chr1 200 400

indels file:

chr1 120 150 deletion

output exome bed file:

chr1 10 100
chr1 170 370

[Devon Ryan]

You might have to write a little program to do this for you. Thankfully with just BED files this is rather more doable.

[ersgupta]

Yeah, was planning to do that. But just thought to ask if anyone already has a script for this. It would be great if there was something like FastaAlternateReferenceMaker for bed files, I guess will have to write on my own.